Abstract The share of organic dairy production in EU is increasing and this study describes the herd structure and cow performance in organic and conventional dairy production systems in Sweden. The data included records from 2 902 718 lactations, collected in organic ( n = 471) and conventional ( n = 13 976) herds between 1998 and 2005. Compared with conventional herds, the organic herds were larger and increased more rapidly in size. The replacement rate was slightly lower in organic herds and fewer Swedish Holsteins were used. The statistical analysis of cow performance in the first three lactations showed lower milk, fat and protein production in organic herds, but the increase in production from first to second lactation was larger when expressed in kg milk. Fertility was better for organically managed cows compared to conventionally managed cows, but the somatic cell count (SCC) was higher. However, at a given production level the fertility was slightly worse in organic herds while there was no difference in SCC. No interactions of importance were found between production system and breed for any trait. The results showed that organic and conventional dairy production differed regarding herd structure and cow performance. However, the differences in fertility and SCC found were to a high extent explained by the lower milk yield in organic production and no breed was found to perform better in either system.