We have conducted a project to develop a common protocol for indoor environmental quality (IEQ) assessment and to assess the effects of energy retrofits on IEQ. This paper focuses on thermal comfort, which was first assessed based on 2-month continuous monitoring in 16 multi-family buildings (94 apartments) in Finland and 20 buildings (96 apartments) in Lithuania during heating season before retrofits. In addition, corresponding data after retrofits were available from three buildings (17 apartments) from Finland and seven (30 apartments) from Lithuania. Two data loggers per apartment were placed to evaluate Tw and RHw (warm area), and Tc and RHc (coldest spot). Questionnaire data regarding housing quality and health were collected from the occupants. The results before retrofits indicated high Tw (>23°C) for a large proportion of time in Finnish apartments, whereas opposite trend was observed in Lithuania. After retrofits, proportion of time with high Tw was higher while proportion of apartments with low RHw was lower in Finland, whereas in Lithuania, about one fourth of the apartments had higher Tw and RHw, hence fulfilling the national guidelines. The average absolute humidity was higher after retrofits in both countries, especially in Lithuania (by 15%). Occupant responses indicated improved thermal comfort. Therefore, potential effects of energy retrofits on occupants’ thermal environment and satisfaction were demonstrated, and simply adjusting indoor temperature could help to save energy. Further analysis is needed to include the effects of outdoor conditions, as well as overall IEQ to the assessment.