Biomass production of weeds under two crop management systems was compared. The conventional system relied on artificial fertilizers and herbicides, and the other was a low-input system incorporating manure as a fertilizer without use of herbicides. A five-year crop rotation comprising rye, oat-pea, barley and two-year grasslands was used in both cropping systems. The air-dried weight of weed species and crop, as well as the crop yield, were determined each year from barley, oat-pea and rye field strips between 1992 and 2000. The total biomass of weeds and the biomass of annual weeds alone were higher in low-input cropping than in conventional cropping only in rye and barley fields. The biomass production of perennial weeds did not differ between systems in any crop. The yield and the biomass of crops was higher in conventional than in low-input cropping for each crop. In both systems perennial species dominated the weed community in most years. However, dominance of perennials as well as variation in the weed biomasses among years was more marked for conventional than for low-input cropping. The clear dominance of a perennial weed species, Elymus repens, resulted in a more skewed distribution of abundance for conventional than for low-input crop management systems. E. repens was the only species that was more abundant in conventional than in low-input cropping. The most abundant species were largely similar in both systems. In general, the species composition differed more between autumn (rye) and spring-sown crops (barley and oat-pea) than between crop management systems. The weed community of rye fields was characterized by several perennial species and some autumn germinating annuals. This pattern was observed especially in low-input fields.