An epidemiological investigation of an outbreak of intestinal atresia in Israeli Holstein-Friesian newborn calves showed a linkage with rectal palpation for early pregnancy diagnosis, performed less than 42 days after insemination. The odds of an exposed calf, i.e., one born to a dam that was diagnosed by early palpation as having intestinal atresia were 119.7 times higher than one born in normal control herds (95% CI; 7.4-1946.3). A total of 682 calves-at-risk was recorded from mid-1998 to mid-2000 and a total of 47 calves (6.9%) were born with intestinal atresia during this period. Two forms of intestinal atresia were recognized at post-mortem: atresia coli and atresia ilei.