diff --git a/app/Main.hs b/app/Main.hs
--- a/app/Main.hs
+++ b/app/Main.hs
@@ -31,13 +31,16 @@
                                      <?> "([,] | CHAR) The delimiter of the CSV file. Format is name,replicate,value."
                        , sortType         :: Maybe Sort
                                      <?> "([Ascending] | Descending) Ascending ranks 1 as the lowest value while Descending ranks the highest value as 1."
+                       , defaultValue     :: Maybe Double
+                                     <?> "([Nothing] | DOUBLE) Default value of missing replicate rather than removing entity."
                        }
                deriving (Generic)
 
 modifiers :: Modifiers
 modifiers = lispCaseModifiers { shortNameModifier = short }
   where
-    short x         = firstLetter x
+    short "defaultValue" = Just 'v'
+    short x              = firstLetter x
 
 instance ParseField Sort
 
@@ -55,6 +58,7 @@
         delim'        =
             Delimiter . fromMaybe ',' . unHelpful . delimiter $ opts
         sortType'     = fromMaybe Ascending . unHelpful . sortType $ opts
+        defaultValue' = fmap DefaultValue . unHelpful . defaultValue $ opts
         decodeOpt       = CSV.defaultDecodeOptions
                             { CSV.decDelimiter =
                                 fromIntegral (ord . unDelimiter $ delim')
@@ -64,7 +68,7 @@
                                 fromIntegral (ord . unDelimiter $ delim')
                             }
 
-    entities <- loadNamedEntities
+    entities <- loadNamedEntities defaultValue'
               . either error snd
               . CSV.decodeByNameWith decodeOpt
             <$> B.getContents
diff --git a/rank-product.cabal b/rank-product.cabal
--- a/rank-product.cabal
+++ b/rank-product.cabal
@@ -1,5 +1,5 @@
 name:                rank-product
-version:             0.2.1.1
+version:             0.2.2.0
 synopsis:            Find the rank product of a data set.
 description:         Find the rank product of a data set and get the p-value from a permutation test.
 homepage:            http://github.com/GregorySchwartz/rank-product#readme
diff --git a/src/Statistics/Load.hs b/src/Statistics/Load.hs
--- a/src/Statistics/Load.hs
+++ b/src/Statistics/Load.hs
@@ -12,10 +12,11 @@
     ) where
 
 -- Standard
-import Data.List (sort)
+import Data.List (sort, find)
 import qualified Data.Foldable as F
 import qualified Data.Map.Strict as Map
 import qualified Data.Sequence as Seq
+import qualified Data.Set as Set
 import qualified Data.Text as T
 import qualified Data.Text.Read as T
 import qualified Data.Vector as V
@@ -26,14 +27,18 @@
 import Statistics.Types
 
 -- | Load entities from a list of rows.
-loadNamedEntities :: V.Vector (Map.Map T.Text T.Text) -> [NamedEntity]
-loadNamedEntities = fmap (uncurry NamedEntity)
-                  . Map.toAscList
-                  . Map.map (fmap snd . sort . F.toList)
-                  . Map.fromListWith (Seq.><)
-                  . fmap lookupInfo
-                  . V.toList
+loadNamedEntities ::
+  Maybe DefaultValue -> V.Vector (Map.Map T.Text T.Text) -> [NamedEntity]
+loadNamedEntities defVal rows =
+  fmap (uncurry NamedEntity)
+    . Map.toAscList
+    . Map.map (fmap snd . supplyReplicates defVal allReplicates . F.toList)
+    . Map.fromListWith (Seq.><)
+    . fmap lookupInfo
+    . V.toList
+    $ rows
   where
+    allReplicates = Set.fromList . fmap (lookupErr "replicate") . V.toList $ rows
     lookupErr x = Map.findWithDefault (error $ "Missing column: " <> show x) x
     lookupInfo m =
       ( Name $ lookupErr "name" m
@@ -41,3 +46,15 @@
                       , either error fst . T.double $ lookupErr "value" m
                       )
       )
+
+-- | Give a default value to missing replicates.
+supplyReplicates :: Maybe DefaultValue
+                 -> Set.Set T.Text
+                 -> [(T.Text, Double)]
+                 -> [(T.Text, Double)]
+supplyReplicates Nothing _ xs = sort xs
+supplyReplicates (Just (DefaultValue defVal)) allReplicates xs =
+    Map.toAscList . F.foldl' supply repMap . Set.toList $ allReplicates
+  where
+    supply m x = if Map.member x m then m else Map.insert x defVal m
+    repMap = Map.fromList xs
diff --git a/src/Statistics/Types.hs b/src/Statistics/Types.hs
--- a/src/Statistics/Types.hs
+++ b/src/Statistics/Types.hs
@@ -20,6 +20,7 @@
 newtype Delimiter         = Delimiter { unDelimiter :: Char } deriving (Read, Show)
 newtype Name              = Name { unName :: T.Text } deriving (Eq, Ord, Show)
 newtype Permutations      = Permutations Int deriving (Show)
+newtype DefaultValue      = DefaultValue Double
 newtype Entity            = Entity { unEntity :: [Double] } deriving (Show)
 newtype RankEntity        = RankEntity { unRankEntity :: [Double] } deriving (Show)
 newtype RankProductEntity = RankProductEntity