BACKGROUND: The possible association between maternal appendicitis/appendectomy during pregnancy and congenital abnormalities in the offspring was studied. CASES: Two cases with primary microcephaly were born to mothers who had complicated appendicitis owing to the delay of appendectomy resulting in abscess/peritonitis associated with septicemia and fever in the second trimester of pregnancy. CONCLUSIONS: Delay in surgical intervention of appendicitis in pregnancy can result in maternal morbidity that may be associated with primary microcephaly in the offspring. Birth Defects Research (Part A), 2009. © 2009 Wiley-Liss, Inc.