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Leek (Allium porrum L.) is an important outdoor vegetable in West Europe, where it is cultivated on about 30,000 ha. Most commercial cultivars of leek are open pollinated. One of the major problems with the crop is poor uniformity. Leek is an outbreeding species with up to 20% self-fertilisation. Much of the variation of open pollinated cultivars is explained by the strong sensitivity to inbreeding depression after selfing. In this study we attempt to analyse in a systematic way the relationship between degree of selfing and agricultural performance in leek. The results obtained confirm a negative correlation between selfing and some agricultural aspects important for vigour such as seedling emergence, plant growth and plant fresh yield. Also negative correlations between degree of selfing and seed individual weight and between selfing and seed individual size were found. The negative relationship between inbreeding and plant weight at harvest is further confirmed in an experiment in which the origin (cross-pollination or self-pollination) of each individual offspring plant analysed was determined using AFLP-markers. Finally, the correlation between chlorophyll deficiency genes and the loss of vigour that follows selfing was investigated. The results obtained demonstrate a significant decrease of pigment content in two generations of selfing.