The aim of this paper is to assess the impact that pollutant sources and ventilation strategies have on thermal comfort levels and indoor air quality (IAQ) in low energy houses through a case study using the detailed thermal simulation program, ESP-r. CO2 is commonly used as a proxy for IAQ, but a novelty of this research is the integrated analysis of distribution for other pollutants, specifically formaldehyde. A model was created based on monitored data from a low energy house. Acceptance criteria for calibrating the model were defined, addressing the current absence of specific guidelines for model calibration based on the monitored indoor environment. Then, a review of current literature of indoor pollutants was undertaken and three time-dependent models were implemented in ESP-r to model formaldehyde emissions. Different scenarios were defined to investigate specific design questions and common ventilation issues regarding the indoor environmental quality (IEQ). The results demonstrate that detailed modelling and simulation can predict IEQ issues and help to design ventilation strategies in low energy houses.