An agar gel immunodiffusion (AGID) test was used over a 3-year period to examine 1,871 serum samples from sheep representing 5 Mycobacterium paratuberculosis-infected flocks and 4 flocks presumed to be uninfected. Of 1,032 sheep, 31 had positive AGID test results (scoring 1 to 5), and 23 of these 31 were necropsied. Infection with M paratuberculosis was confirmed by 1 or more of the following findings: observation of typical lesions on histologic examination of sections of ileum or ileocecal lymph nodes, observation of clumps of acid-fast bacteria in mucosal smears of ileum, and isolation of the organism from feces or tissue. False-positive results on AGID testing were not found in sheep from flocks known to have exposure to Corynebacterium pseudotuberculosis. Diarrhea in infected sheep was observed infrequently; chronic, severe weight loss was the most common sign observed. On histologic examination of tissues from 20 infected sheep, 16 (80%) had diffuse lesions of the ileum and 13 (65%) had acid-fast bacteria in areas of ileal inflammation; 4 had discrete granulomas and peripheral lymphocytic infiltrates in the ileum. Sheep with diffuse lesions tended to have higher mean scores on AGID testing and examination for acid-fast bacteria, compared with those from sheep with more discrete lesions. Bacteriologic culture yielded M paratuberculosis from only 3 sheep with paratuberculosis.(ABSTRACT TRUNCATED AT 250 WORDS)