Background: Caenorhabditis elegans is a major model system in biology, yet very little is known about its biology outside the laboratory. Especially, its unusual mode of reproduction with self-fertile hermaphrodites and facultative males raises the question of its frequency of outcrossing in natural populations. Results: We describe the first analysis of C. elegans individuals sampled directly from natural populations. C. elegans is found predominantly in the dauer stage and with a very low frequency of males compared with hermaphrodites. While C. elegans was previously shown to display a low worldwide genetic diversity, we find by comparison a surprisingly high local genetic diversity of C. elegans populations; this local diversity is contributed in great part by immigration of new alleles rather than by mutation. Our results on heterozygote frequency, male frequency and linkage disequilibrium furthermore show that selfing is the predominant mode of reproduction in C. elegans natural populations, yet that infrequent outcrossing events occur, at a rate of approximately 1%. Conclusions: Our results give a first insight in the biology of C. elegans in the natural populations. They demonstrate that local populations of C. elegans are genetically diverse and that a low frequency of outcrossing allows for the recombination of these locally diverse genotypes.