The aim of this study was to evaluate the follow-up effect of biowaste compost on the structure and macroporosity of soil two years after compost application. The results were compared with mineral nitrogen fertilization and untreated control. A long-term crop rotation experiment was established on a silty loam Molli-gleyic Fluvisol in eastern Austria. In the 13-year field experiment different rates of compost and nitrogen fertilizers were applied. The compost used was source-separated organic house- hold waste compost at rates of 7, 13 and 18 t ha-1 year-1 on average. Nitrogen fertilization was applied to supply 27, 47 and 64 kg N ha-1 year-1 on average. Undisturbed soil samples were collected in March 2005 and July 2005 from the 10-20 cm soil layer, and characteristics of macropores were determined with special focus on biopores content. Results showed that the long-term application of compost and nitrogen fertilizer in the investigated soil did not cause any significant influence on macropore volume. The only effect of compost and nitrogen fertilization was observed in biopores content. Nitrogen fertilization increased participation of biopores of 1000-2000 m and 2000-4000 m in diameter with respect to control and compost treatment. This effect can be ascribed to higher plant biomass production at the nitrogen fertilization treatment.