This article analyzes in detail the impact of wooden houses on the environment using the life cycle assessment (LCA) methodology and at the same time evaluates the indoor environmental quality (IEQ) in these houses. The investigated detached family houses had a wooden structure. The first one had a bearing system made of a wooden frame; other materials were conventional. The second house was built entirely of log wood. Given the high risk of greenhouse gas emissions, the concentration of which in the atmosphere is causing global climate change, the global warming potential (GWP) indicator is crucial. According to results, the family house built entirely of wood and with a biomass boiler significantly reduces CO2 emissions and is therefore considered from the LCA point of view as a more suitable alternative compared to a house with a wooden frame structure. The building materials with the highest share involved in the creation of GWP include concrete structures (38–48%), ceramic roof tiles (33%) and plasterboard (15%). Plasterboard cladding (55%), concrete structures (17–19%), oriented strand board OSB (9–22%), impregnated wooden structures (31–52%) and plastic windows (9%) are the most involved in acidification potential (AP) and eutrophication potential (EP). Plasterboard structures (21%), impregnated wood materials (47.4%), reinforced concrete structures (12%) and mineral wool and roof tiles significantly contribute to the creation of photochemical ozone creation potential (POCP) and ozone depletion potential (ODP). The indoor environmental quality was evaluated through short-term measurements of basic physico-chemical parameters. Since both houses have different characteristics, the aim of this monitoring was to evaluate the actual state of IEQ in selected wooden houses under real conditions. Based on the recorded results, it can be stated that neither presented wooden house, in terms of thermal-humidity microclimate, concentration of CO2 and particulate matter, represents an environment with a negative impact on their occupants. With regards to volatile organic compounds (VOCs), the increased concentrations of xylenes and tetrachlorethylene in the log house were probably caused by the application of impregnation and protective coatings six months before monitoring. In this case, the concentration of tetrachloroethene, which is considered a potential carcinogen, was six times higher than the legislative limit. For VOCs, such as limonene, isobutylene and n-butylacetate, which were found in the wooden frame house, no limits are set. The legislative limits for xylenes and tetrachlorethylene in this house have not been exceeded, and therefore the IEQ cannot yet be considered harmful for health. The presence of all the mentioned VOCs in the interior air of the wooden frame house is more related to the activities of occupants, as this house has been inhabited for several years.