Solanum tuberosum cultivars, Solanum tuberosum × Solanum tuberosum subsp. andigena hybrids and breeding clones with different time to maturity were screened for drought tolerance in field plots located in the coastal desert of Peru. Variation for drought tolerance was illustrated by clone-dependent differences in tuber yield and yield loss under drought conditions. Neither changes in stomatal conductance nor maximum quantum yield of chlorophyll fluorescence were quantitatively associated with yield or yield loss under drought. In contrast, relative vegetation index (reflectance at 800 nm / reflectance at 650 nm) and normalized difference vegetation index [(reflectance at 800 nm -reflectance at 650 nm) / (reflectance at 800 nm + reflectance at 650 nm)] on day 25 and day 40 after drought were correlated with yield. The vegetation indices are related to leaf area index and above ground biomass, which appeared to be major determinants for yield in the tested cultivars under drought. Nitrate reductase activity was significantly decreased in drought-exposed plants, but activity depletion was independent of yield or yield maintenance. Putative drought tolerance genes were differentially expressed in leaves of water stressed genotypes. Induction of the protein phosphatase 2C gene was positively associated with yield maintenance under drought. Furthermore, Potato Research (2007) 50:71-85