Little is known about effects of public use of antimicrobial handwashing soap. A double-blinded, randomized clinical trial of hands of primary caretakers in 238 inner city households was conducted in which effects of plain or antimicrobial (containing 0.2% triclosan) handwashing soap on bacterial counts of the hands were compared before and after a single wash and before and after handwashing following a year of product use. The randomly assigned product was provided without cost to each household during monthly home visits, and compliance with product use was monitored. Households were contacted by telephone weekly and with a home visit monthly for 11 months. Hand cultures were obtained before and after handwashing at baseline and after 11 months, using a modified glove juice technique. Overall, there were no significant differences in pre-to-post handwashing counts at baseline (p = 0.41), but by the end of one year, post-wash counts were significantly lower than pre-wash (p = 0.000) for those using either antimicrobial or plain soap. There were no significant differences in mean log counts either before or after handwashing between those using the antimicrobial or plain soap at baseline or after a year of use (all p values > 0.28). For the group using antimicrobial soap, higher counts were observed post-handwashing in 31.3% of paired samples at baseline and 26.7% after one year (p = 0.03). A single handwash had minimal effect on quantity of hand flora, but there were significant effects over time, regardless of whether antimicrobial or plain soap was used. In the absence of more definitive evidence, the risk-benefit ratio argues in favor of targeted rather than ubiquitous, general household use of antimicrobial soap.