While the majority of studies of social capital and health have focused on conceptualizing social capital at the geographic level, evidence remains sparse on workplace social capital. We examined the association between workplace social capital and health status among Japanese private sector employees in a cross-sectional study. By employing a two-stage stratified random sampling procedure, 1147 employees were identified from 46 companies in Okayama in 2007. Workplace social capital was measured based on two components; trust and reciprocity. Company-level social capital was based on aggregating employee responses and calculating the proportion of workers reporting mistrust and lack of reciprocity. Multilevel logistic regression analysis was conducted using Markov Chain Monte Carlo methods to explore whether individual- and company-level mistrust and lack of reciprocity were associated with poor self-rated health. Odds ratios (ORs) and 95% credible intervals (CIs) for poor health were obtained for each variable. Workers reporting individual-level mistrust and lack of reciprocity had approximately double the odds of poor health even after controlling for sex, age, occupation, educational attainment, smoking, alcohol use, physical activity, body mass index, and chronic diseases. While we found some suggestion of a contextual association between company-level mistrust and poor health, no association was found between company-level lack of reciprocity and health. Despite the thorough examination of cross-level interaction terms between company-level social capital and individual characteristics, no clear patterns were observed. Individual perceptions of mistrust and lack of reciprocity at work have adverse effects on self-rated health among Japanese workers. Although the present study possibly suggests the contextual effect of workplace mistrust on workers' health, the contextual effect of workplace lack of reciprocity was not supported.