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In the Azapa Valley, near the Atacama desert in the far north of Chile, the climate allows cultivation of year-round vegetable crops, especially during the winter (from June to September). Tomato is the main crop in this region. The goal of this study was twofold: to evaluate the effects of an inert substrate (perlite) and an organic substrate (compost) on the yield and quality of cherry (cv. 51-72) and cv. Naomi tomatoes in soil-less culture and to compare a high-tech greenhouse with another, more economical shade-house constructed of anti-insect mesh. A standard nutrient solution at pH 5.8 with an electrical conductivity of 2.2 dS m(-1) was used. The control parameters in the fertigation were the following: the electrical conductivity, the pH, and the percentage of the applied volume that was measured as drainage. Yield (the mean weight and number of fruits) and quality (the soluble solid matter, firmness and percentage of dry material) measurements were taken of the fruit. The climate inside each greenhouse was distinct, although neither the temperature nor the relative humidity limited the tomato growth. The values for the fertigation control parameters were very different for the two substrates, but, in general, the yields and quality parameters were very similar. The data suggested that compost, as used directly as a substrate, is an alternative to more traditional inorganic substrates, such as perlite. We also found that a mesh (anti-insect) greenhouse is a viable, less expensive alternative for growing tomatoes in the majority of the Arica region.