diff --git a/web/src/components/Common/Checkbox.tsx b/web/src/components/Common/Checkbox.tsx
index 8c51af6e..7627208d 100644
--- a/web/src/components/Common/Checkbox.tsx
+++ b/web/src/components/Common/Checkbox.tsx
@@ -1,5 +1,6 @@
-import React, { PropsWithChildren, ReactNode, useCallback } from 'react'
-import { FormGroup as FormGroupBase, Input, Label as LabelBase } from 'reactstrap'
+import React, { PropsWithChildren, ReactNode, useCallback, useEffect, useMemo, useRef } from 'react'
+import type { StrictOmit } from 'ts-essentials'
+import { FormGroup as FormGroupBase, Input, InputProps, Label as LabelBase } from 'reactstrap'
 import styled from 'styled-components'
 import type { SetterOrUpdater } from 'src/types'
 
@@ -57,6 +58,54 @@ export function CheckboxWithIcon({ title, label, icon, checked, setChecked }: Ch
   )
 }
 
+export enum CheckboxState {
+  Checked,
+  Unchecked,
+  Indeterminate,
+}
+
+export interface CheckboxIndeterminateProps extends StrictOmit<InputProps, 'onChange' | 'checked'> {
+  state?: CheckboxState
+  onChange?(state: CheckboxState): void
+}
+
+/** Checkbox with 3 states: checked, unchecked, indeterminate */
+export function CheckboxIndeterminate({ state, onChange, ...restProps }: CheckboxIndeterminateProps) {
+  const inputRef = useRef<HTMLInputElement>(null)
+
+  const handleOnChange = useCallback(() => {
+    if (state === CheckboxState.Checked) {
+      return onChange?.(CheckboxState.Unchecked)
+    }
+    return onChange?.(CheckboxState.Checked)
+  }, [onChange, state])
+
+  useEffect(() => {
+    if (inputRef?.current) {
+      inputRef.current.indeterminate = state === CheckboxState.Indeterminate
+    }
+  }, [state])
+
+  const checked = useMemo(() => state === CheckboxState.Checked, [state])
+
+  return <Input {...restProps} type="checkbox" innerRef={inputRef} checked={checked} onChange={handleOnChange} />
+}
+
+export interface CheckboxIndeterminateWithTextProps extends Omit<CheckboxIndeterminateProps, 'children'> {
+  label: string
+}
+
+export function CheckboxIndeterminateWithText({ label, title, ...restProps }: CheckboxIndeterminateWithTextProps) {
+  return (
+    <FormGroup check title={title}>
+      <Label check>
+        <CheckboxIndeterminate {...restProps} />
+        <CheckboxText>{label}</CheckboxText>
+      </Label>
+    </FormGroup>
+  )
+}
+
 const FormGroup = styled(FormGroupBase)`
   overflow-x: hidden;
 `
diff --git a/web/src/components/Sidebar/SidebarSectionGeography.tsx b/web/src/components/Sidebar/SidebarSectionGeography.tsx
index 9e2fef38..873e2f85 100644
--- a/web/src/components/Sidebar/SidebarSectionGeography.tsx
+++ b/web/src/components/Sidebar/SidebarSectionGeography.tsx
@@ -1,20 +1,14 @@
-import { sortBy } from 'lodash-es'
+import { isEmpty, sortBy } from 'lodash-es'
 import React, { useMemo } from 'react'
 import dynamic from 'next/dynamic'
-import { useRecoilState, useSetRecoilState } from 'recoil'
+import { useRecoilState } from 'recoil'
 import styled from 'styled-components'
-import { Button, Col, Form, FormGroup, Row } from 'reactstrap'
+import { Form } from 'reactstrap'
 import { useTranslationSafe } from 'src/helpers/useTranslationSafe'
 import { Pathogen, usePathogen, useRegionsDataQuery } from 'src/io/getData'
 import { fuzzySearchObj } from 'src/helpers/fuzzySearch'
-import {
-  continentAtom,
-  countryAtom,
-  geographyDisableAllAtom,
-  geographyEnableAllAtom,
-  geographySearchTermAtom,
-} from 'src/state/geography.state'
-import { CheckboxWithIcon } from 'src/components/Common/Checkbox'
+import { continentAtom, countryAtom, geographyEnableAllAtom, geographySearchTermAtom } from 'src/state/geography.state'
+import { CheckboxIndeterminateWithText, CheckboxWithIcon } from 'src/components/Common/Checkbox'
 import { transliterate } from 'transliteration'
 
 const GeoIconCountry = dynamic(() => import('src/components/Common/GeoIconCountry').then((m) => m.GeoIconCountry))
@@ -61,12 +55,18 @@ export function SidebarSectionGeography({ pathogenName }: SidebarSectionGeograph
         }),
       ),
     ]
-    return sortBy(scored, ({ score }) => score).map(({ component }) => component)
-  }, [countries, pathogenName, regions, searchTerm, t])
+
+    const checkboxes = sortBy(scored, ({ score }) => score).map(({ component }) => component)
+
+    if (isEmpty(searchTerm)) {
+      checkboxes.unshift(<GeographySelectAll key="GeographySelectAll" pathogen={pathogen} />)
+    }
+
+    return checkboxes
+  }, [countries, pathogen, pathogenName, regions, searchTerm, t])
 
   return (
     <Container>
-      <GeographySelectAll pathogen={pathogen} />
       <Form>{checkboxes}</Form>
     </Container>
   )
@@ -78,21 +78,14 @@ export interface GeographySelectAllProps {
 
 export function GeographySelectAll({ pathogen }: GeographySelectAllProps) {
   const { t } = useTranslationSafe()
-  const selectAll = useSetRecoilState(geographyEnableAllAtom(pathogen.name))
-  const deselectAll = useSetRecoilState(geographyDisableAllAtom(pathogen.name))
+  const [isAllEnabled, setIsAllEnabled] = useRecoilState(geographyEnableAllAtom(pathogen.name))
   return (
-    <Row noGutters>
-      <Col className="d-flex">
-        <FormGroup className="flex-grow-0 mx-auto">
-          <Button type="button" color="link" onClick={selectAll}>
-            {t('Select all')}
-          </Button>
-          <Button type="button" color="link" onClick={deselectAll}>
-            {t('Deselect all')}
-          </Button>
-        </FormGroup>
-      </Col>
-    </Row>
+    <CheckboxIndeterminateWithText
+      label={t('Select all')}
+      title={t('Select all')}
+      state={isAllEnabled}
+      onChange={setIsAllEnabled}
+    />
   )
 }
 
diff --git a/web/src/components/Sidebar/SidebarSectionVariants.tsx b/web/src/components/Sidebar/SidebarSectionVariants.tsx
index 8e5e0f5b..36629576 100644
--- a/web/src/components/Sidebar/SidebarSectionVariants.tsx
+++ b/web/src/components/Sidebar/SidebarSectionVariants.tsx
@@ -1,14 +1,15 @@
 import React, { useMemo } from 'react'
-import { Button, Col, Form, FormGroup, Row } from 'reactstrap'
-import { useRecoilState, useSetRecoilState } from 'recoil'
+import { Form } from 'reactstrap'
+import { useRecoilState } from 'recoil'
 import styled from 'styled-components'
 import { ColoredBox } from 'src/components/Common/ColoredBox'
 import { fuzzySearch } from 'src/helpers/fuzzySearch'
 import { useTranslationSafe } from 'src/helpers/useTranslationSafe'
 import { Pathogen, usePathogen, useVariantsDataQuery, useVariantStyle } from 'src/io/getData'
 import { variantsSearchTermAtom } from 'src/state/geography.state'
-import { variantAtom, variantsDisableAllAtom, variantsEnableAllAtom } from 'src/state/variants.state'
-import { CheckboxWithIcon } from 'src/components/Common/Checkbox'
+import { variantAtom, variantsEnableAllAtom } from 'src/state/variants.state'
+import { CheckboxIndeterminateWithText, CheckboxWithIcon } from 'src/components/Common/Checkbox'
+import { isEmpty } from 'lodash-es'
 
 const Container = styled.div`
   display: flex;
@@ -23,16 +24,17 @@ export function SidebarSectionVariants({ pathogenName }: SidebarSectionVariantsP
   const pathogen = usePathogen(pathogenName)
   const { variants } = useVariantsDataQuery(pathogenName)
   const [searchTerm] = useRecoilState(variantsSearchTermAtom)
-  const checkboxes = useMemo(
-    () =>
-      fuzzySearch(variants, searchTerm).map(({ item }) => (
-        <VariantsCheckbox pathogenName={pathogenName} key={item} variant={item} />
-      )),
-    [pathogenName, searchTerm, variants],
-  )
+  const checkboxes = useMemo(() => {
+    const checkboxes = fuzzySearch(variants, searchTerm).map(({ item }) => (
+      <VariantsCheckbox pathogenName={pathogenName} key={item} variant={item} />
+    ))
+    if (isEmpty(searchTerm)) {
+      checkboxes.unshift(<VariantsSelectAll key="VariantsSelectAll" pathogen={pathogen} />)
+    }
+    return checkboxes
+  }, [pathogen, pathogenName, searchTerm, variants])
   return (
     <Container>
-      <VariantsSelectAll pathogen={pathogen} />
       <Form>{checkboxes}</Form>
     </Container>
   )
@@ -44,21 +46,14 @@ export interface VariantsSelectAllProps {
 
 export function VariantsSelectAll({ pathogen }: VariantsSelectAllProps) {
   const { t } = useTranslationSafe()
-  const selectAll = useSetRecoilState(variantsEnableAllAtom(pathogen.name))
-  const deselectAll = useSetRecoilState(variantsDisableAllAtom(pathogen.name))
+  const [isAllEnabled, setIsAllEnabled] = useRecoilState(variantsEnableAllAtom(pathogen.name))
   return (
-    <Row noGutters>
-      <Col className="d-flex">
-        <FormGroup className="flex-grow-0 mx-auto">
-          <Button type="button" color="link" onClick={selectAll}>
-            {t('Select all')}
-          </Button>
-          <Button type="button" color="link" onClick={deselectAll}>
-            {t('Deselect all')}
-          </Button>
-        </FormGroup>
-      </Col>
-    </Row>
+    <CheckboxIndeterminateWithText
+      label={t('Select all')}
+      title={t('Select all')}
+      state={isAllEnabled}
+      onChange={setIsAllEnabled}
+    />
   )
 }
 
diff --git a/web/src/state/geography.state.ts b/web/src/state/geography.state.ts
index f3135b55..774aa2c8 100644
--- a/web/src/state/geography.state.ts
+++ b/web/src/state/geography.state.ts
@@ -5,7 +5,7 @@ import { GeographyData } from 'src/io/getData'
 import { getDataRootUrl } from 'src/io/getDataRootUrl'
 import urljoin from 'url-join'
 import { isDefaultValue } from 'src/state/utils/isDefaultValue'
-import { ErrorInternal } from 'src/helpers/ErrorInternal'
+import { CheckboxState } from 'src/components/Common/Checkbox'
 
 const geographyAtom = atomFamily<GeographyData, string>({
   key: 'geographyAtom',
@@ -91,33 +91,47 @@ export const countryAtom = selectorFamily<boolean, { pathogen: string; country:
     },
 })
 
+function isEnabledAll<T extends { enabled: boolean }>(items: T[]) {
+  return items.every((item) => item.enabled)
+}
+
+function isDisabledAll<T extends { enabled: boolean }>(items: T[]) {
+  return items.every((item) => !item.enabled)
+}
+
 function setEnabledAll<T extends { enabled: boolean }>(items: T[], enabled: boolean) {
   return items.map((item) => ({ ...item, enabled }))
 }
 
-export const geographyEnableAllAtom = selectorFamily<unknown, string>({
+export const geographyEnableAllAtom = selectorFamily<CheckboxState, string>({
   key: 'geographyEnableAllAtom',
-  get() {
-    throw new ErrorInternal("Attempt to read from write-only atom: 'geographyEnableAllAtom'")
-  },
-  set:
+  get:
     (region) =>
-    ({ get, set }) => {
-      set(countriesAtom(region), setEnabledAll(get(countriesAtom(region)), true))
-      set(continentsAtom(region), setEnabledAll(get(continentsAtom(region)), true))
+    ({ get }) => {
+      const countries = get(countriesAtom(region))
+      const regions = get(continentsAtom(region))
+      const locations = [...regions, ...countries]
+      if (isEnabledAll(locations)) {
+        return CheckboxState.Checked
+      }
+      if (isDisabledAll(locations)) {
+        return CheckboxState.Unchecked
+      }
+      return CheckboxState.Indeterminate
     },
-})
-
-export const geographyDisableAllAtom = selectorFamily<unknown, string>({
-  key: 'geographyDisableAllAtom',
-  get() {
-    throw new ErrorInternal("Attempt to read from write-only atom: 'geographyDisableAllAtom'")
-  },
   set:
     (region) =>
-    ({ get, set }) => {
-      set(countriesAtom(region), setEnabledAll(get(countriesAtom(region)), false))
-      set(continentsAtom(region), setEnabledAll(get(continentsAtom(region)), false))
+    ({ get, set, reset }, value) => {
+      if (isDefaultValue(value)) {
+        reset(countriesAtom(region))
+        reset(continentsAtom(region))
+      } else if (value === CheckboxState.Checked) {
+        set(countriesAtom(region), setEnabledAll(get(countriesAtom(region)), true))
+        set(continentsAtom(region), setEnabledAll(get(continentsAtom(region)), true))
+      } else if (value === CheckboxState.Unchecked) {
+        set(countriesAtom(region), setEnabledAll(get(countriesAtom(region)), false))
+        set(continentsAtom(region), setEnabledAll(get(continentsAtom(region)), false))
+      }
     },
 })
 
diff --git a/web/src/state/variants.state.tsx b/web/src/state/variants.state.tsx
index 35dd2da9..a270faa4 100644
--- a/web/src/state/variants.state.tsx
+++ b/web/src/state/variants.state.tsx
@@ -5,7 +5,7 @@ import { VariantsData } from 'src/io/getData'
 import { getDataRootUrl } from 'src/io/getDataRootUrl'
 import urljoin from 'url-join'
 import { isDefaultValue } from 'src/state/utils/isDefaultValue'
-import { ErrorInternal } from 'src/helpers/ErrorInternal'
+import { CheckboxState } from 'src/components/Common/Checkbox'
 
 const variantDataAtom = atomFamily<VariantsData, string>({
   key: 'variantDataAtom',
@@ -52,30 +52,41 @@ export const variantAtom = selectorFamily<boolean, { pathogen: string; variant:
     },
 })
 
+function isEnabledAll<T extends { enabled: boolean }>(items: T[]) {
+  return items.every((item) => item.enabled)
+}
+
+function isDisabledAll<T extends { enabled: boolean }>(items: T[]) {
+  return items.every((item) => !item.enabled)
+}
+
 function setEnabledAll<T extends { enabled: boolean }>(items: T[], enabled: boolean) {
   return items.map((item) => ({ ...item, enabled }))
 }
 
-export const variantsEnableAllAtom = selectorFamily<unknown, string>({
+export const variantsEnableAllAtom = selectorFamily<CheckboxState, string>({
   key: 'variantsEnableAllAtom',
-  get() {
-    throw new ErrorInternal("Attempt to read from write-only atom: 'variantsEnableAllAtom'")
-  },
-  set:
+  get:
     (region) =>
-    ({ get, set }) => {
-      set(variantsAtom(region), setEnabledAll(get(variantsAtom(region)), true))
+    ({ get }) => {
+      const variants = get(variantsAtom(region))
+      if (isEnabledAll(variants)) {
+        return CheckboxState.Checked
+      }
+      if (isDisabledAll(variants)) {
+        return CheckboxState.Unchecked
+      }
+      return CheckboxState.Indeterminate
     },
-})
-
-export const variantsDisableAllAtom = selectorFamily<unknown, string>({
-  key: 'variantsDisableAllAtom',
-  get() {
-    throw new ErrorInternal("Attempt to read from write-only atom: 'variantsDisableAllAtom'")
-  },
   set:
     (region) =>
-    ({ get, set }) => {
-      set(variantsAtom(region), setEnabledAll(get(variantsAtom(region)), false))
+    ({ get, set, reset }, value) => {
+      if (isDefaultValue(value)) {
+        reset(variantsAtom(region))
+      } else if (value === CheckboxState.Checked) {
+        set(variantsAtom(region), setEnabledAll(get(variantsAtom(region)), true))
+      } else if (value === CheckboxState.Unchecked) {
+        set(variantsAtom(region), setEnabledAll(get(variantsAtom(region)), false))
+      }
     },
 })