OBJECTIVE To determine whether intrapartum antibiotic prophylaxis for neonatal group B streptococcal (GBS) disease has resulted in an increased rate of non-GBS or antibiotic-resistant early-onset invasive neonatal disease. METHODS Maternal and infant chart review of all infants with bacteria other than GBS isolated from blood or spinal fluid in 1996 through 1999 in 19 hospitals (representing 81% of in-state births to state residents) throughout Connecticut. Suspected cases were identified through clinical microbiology laboratory records or through International Classification of Diseases, Ninth Revision codes when microbiology records were incomplete. RESULTS Ninety-four cases of non-GBS early-onset sepsis or meningitis were detected between 1996 and 1999. The rate of GBS-related early-onset infection (days 0-6 of life) dropped from 0.61/1000 to 0.23/1000 births, but the annual rate of non-GBS sepsis remained steady, ranging from 0.65 to 0.68/1000 during the surveillance period. There was an increase in the proportion of Escherichia coli infections that were ampicillin resistant between 1996 and 1998, but the proportion decreased. in 1999 CONCLUSIONS There was no increase in the incidence of non-GBS early-onset neonatal infections between 1996 and 1999. Fluctuations in the annual incidence of E coli infections, including ampicillin-resistant infections, suggest the need for continuation of surveillance in Connecticut and expansion to monitor larger populations.