diff --git a/include/SalmonDefaults.hpp b/include/SalmonDefaults.hpp
index e5573d9d5..0bfcf31d4 100644
--- a/include/SalmonDefaults.hpp
+++ b/include/SalmonDefaults.hpp
@@ -4,6 +4,7 @@
 namespace salmon {
 namespace defaults {
   // general
+  constexpr const bool discardOrphansAln{false};
   constexpr const bool discardOrphansQuasi{false};
   constexpr const bool allowOrphansFMD{false};
   constexpr const bool seqBiasCorrect{false};
diff --git a/include/SalmonOpts.hpp b/include/SalmonOpts.hpp
index dcad63bb0..b1bbbfbc6 100644
--- a/include/SalmonOpts.hpp
+++ b/include/SalmonOpts.hpp
@@ -260,6 +260,7 @@ struct SalmonOpts {
 
   // for utility (may need to be cleaned up later)
   bool discardOrphansQuasi;
+  bool discardOrphansAln;
   double coverageThresh;
   std::vector<std::string> unmatedReadFiles;
   std::vector<std::string> mate1ReadFiles;
diff --git a/src/ProgramOptionsGenerator.cpp b/src/ProgramOptionsGenerator.cpp
index 590a63dba..411058448 100644
--- a/src/ProgramOptionsGenerator.cpp
+++ b/src/ProgramOptionsGenerator.cpp
@@ -199,6 +199,12 @@ namespace salmon {
     po::options_description alignin("\n"
                                       "alignment input options");
     alignin.add_options()
+    ("discardOrphans",
+       po::bool_switch(&(sopt.discardOrphansAln))->default_value(salmon::defaults::discardOrphansAln),
+       "[Alignment-based mode only] : Discard orphan alignments in the input "
+       ".  If this flag is passed, then only paired alignments will be "
+       "considered toward quantification estimates.  The default behavior is "
+       "to consider orphan alignments if no valid paired mappings exist.")
     ("libType,l", po::value<std::string>()->required(), "Format string describing the library type")
     ("alignments,a", po::value<vector<string>>()->multitoken()->required(),
      "input alignment (BAM) file(s).")
diff --git a/src/SalmonQuantifyAlignments.cpp b/src/SalmonQuantifyAlignments.cpp
index 35c99eaf4..4948de37b 100644
--- a/src/SalmonQuantifyAlignments.cpp
+++ b/src/SalmonQuantifyAlignments.cpp
@@ -163,6 +163,8 @@ void processMiniBatch(AlignmentLibraryT<FragT>& alnLib,
   using salmon::math::logAdd;
   using salmon::math::logSub;
 
+  auto orphanProb = salmonOpts.discardOrphansAln ? LOG_0 : LOG_EPSILON;
+
   // k-mers for sequence bias
   Mer leftMer;
   Mer rightMer;
@@ -289,7 +291,10 @@ void processMiniBatch(AlignmentLibraryT<FragT>& alnLib,
             // If we are expecting a paired-end library, and this is an orphan,
             // then logFragProb should be small
             if (isUnexpectedOrphan(aln, expectedLibraryFormat)) {
-              logFragProb = LOG_EPSILON;
+              logFragProb = orphanProb;
+              if (logFragProb == LOG_0) {
+                continue;
+              }
             }
 
             if (flen > 0.0 and aln->isPaired() and useFragLengthDist and