This study was carried out to measure the mass flow and distribution of nutrients (N, C, S, P, and K) as well as solids and moisture in conventional cage (CC), enriched colony (EC), and aviary (AV) laying-hen houses with Lohmann LSL lite hens located on a commercial laying-hen farm in Iowa. The weight of consumed feed and water, and amounts of eggs and manure production were collected weekly from each house for 2 entire flocks for a total of 28 mo. Samples of feed, egg, manure, litter, and hens were regularly taken and analyzed for total solids and nutrients (N, C, S, P, and K). The nutrient losses to the atmosphere were calculated using a mass balance approach. The losses of nutrients were calculated by subtracting the nutrient contents in eggs, manure, and layer body weight gain from the nutrients intake. The research results showed that the feed intake and manure production rates were similar in the 3 houses. The average nutrient intake in feed, in g d(-1) hen(-1), for the 3 houses was 42.0 C, 2.96 N, 0.36 S, 0.55 P, and 0.79 K. The nutrient intake was partitioned as follow: C - 18% in eggs, 28% in manure, and 54% in air losses; N - 34% in eggs, 58% in manure, and 8% in air losses; S - 26% in eggs, 68% in manure, and 6% in air losses; P - 17% in eggs, 79% in manure, and 3.1% in air losses; and K - 9% in eggs, 89% in manure, and 1.6% in air losses. Manure removed from the EC house was drier than manure from the CC or AV house. Among the 3 hen houses studied, the EC house had the lowest nutrient losses and the AV house had the highest losses. Nutrient loss in CC was statistically similar to EC. But loss of N, C, and S in AV differed from CC and EC. Furthermore, the loss of P and K in the 3 housing systems was statistically similar. The AV had a doubled mortality rate compared to CC and EC.