BACKGROUND: The World Health Organization recommends dry cord care for newborns but this recommendation may not be optimal in low resource settings where most births take place in an unclean environment and infections account for up to half of neonatal deaths. A previous trial in Nepal indicated that umbilical cord cleansing with 4.0% chlorhexidine could substantially reduce mortality and omphalitis risk, but policy changes await additional community-based data. METHODS: The Projahnmo Chlorhexidine study was a three-year, cluster-randomized, community-based trial to assess the impact of three cord care regimens on neonatal mortality and omphalitis. Women were recruited mid-pregnancy, received a basic package of maternal and neonatal health promotion messages, and were followed to pregnancy outcome. Newborns were visited at home by local village-based workers whose areas were randomized to either 1) single- or 2) 7-day cord cleansing with 4.0% chlorhexidine, or 3) promotion of dry cord care as recommended by WHO. All mothers received basic messages regarding hand-washing, clean cord cutting, and avoidance of harmful home-base applications to the cord. Death within 28 days and omphalitis were the primary outcomes; these were monitored directly through home visits by community health workers on days 1, 3, 6, 9, 15, and 28 after birth. DISCUSSION: Due to report in early 2010, the Projahnmo Chlorhexidine Study examines the impact of multiple or single chlorhexidine cleansing of the cord on neonatal mortality and omphalitis among newborns of rural Sylhet District, Bangladesh. The results of this trial will be interpreted in conjunction with a similarly designed trial previously conducted in Nepal, and will have implications for policy guidelines for optimal cord care of newborns in low resource settings in Asia. TRIAL REGISTRATION: ClinicalTrials.gov (NCT00434408).