The aim of this study was to investigate the role of the psychosocial work environment--at the individual level as well as the workplace level--in explaining the variability in the employees' perception of the indoor environment. The perception of the indoor environment was surveyed by questionnaires among 3,281 employees in 39 randomly selected workplaces. Multilevel logistic regression analyses included individual-level and workplace-level covariates to examine the effect of context. Associations between psychosocial risk factors at the workplace level and the employees' perception of the indoor environment was calculated as the interval odds ratios while between-workplace variations were quantified by intraclass correlations and median odds ratios. We found moderate differences between the workplaces in the perception of the indoor environment, but large differences between individuals in the same building indicating that some occupants of a building do perceive problems in the indoor environment even in the absence of a general indoor air problem in the workplace. The type of organisation accounted for some of the variation in perceived indoor environment. Psychosocial work environment factors at the individual level, but not at the workplace-level, were associated with the individual perception of the indoor environment. In addition, an increased tendency to report symptoms was strongly associated with complaints about the indoor environment suggesting bias due to a tendency to "over-report". In studies investigating "sick buildings" contextual factors may be important. Multilevel analyses should be used in future research within workplaces where clustering could be expected.