RT-PCR was used to examine the expression of LAR (encoding the leukocyte-common antigen-related protein tyrosine phosphatase) in normal human colon mucosa, and colon polyps and tumors. Although the LAR protein was not detected in the colon in a previous immunohistochemical study, amplification of a region of LAR between the most membrane proximal (eighth) fibronectin type-III (FN-III) repeat and the transmembrane domain demonstrated LAR expression in all samples, but showed no difference in expression within matched samples from each patient examined. An additional minor fragment amplified in all reactions was consistently observed in colon and various cell line samples using this and two other LAR-specific sets of primers. Cloning and sequencing of the fragment identified it as deriving from a novel alternatively spliced form of LAR containing a retained intron of 85 bp. This intron encodes an additional 13 amino acids followed by an in-frame stop codon, thus its retention is predicted to give rise to a secreted LAR extracellular region isoform(s). LAR transcripts containing the intron were detected by RNase protection assay of colon samples and were present in most human tissues examined by Northern analysis. A protein in colon tumor extract was recognized by antiserum raised to the intron-encoded sequence. Soluble isoforms of the LAR extracellular immunoglobulin (Ig)-like/FN-III repeat-containing region could have a biological function distinct from those isoforms localized at the cell surface and/or coupled to intracellular phosphatase activity.