The development of rice (Oryza sativa L.) cultivars with a higher Zn content in their grains has been suggested as a way to alleviate Zn malnutrition in human populations subsisting on rice in their daily diets. This study was conducted to evaluate the effects of native soil Zn status and fertilizer application on Zn concentrations in grains of five rice genotypes that had previously been identified as either high or low in grain Zn. Genotypes were grown in field trials at four sites ranging in native soil-Zn status from severely deficient to high in plant available Zn. At each site a −Zn plot was compared to a +Zn plot fertilized with 15 kg Zn ha−1. Results showed that native soil Zn status was the dominant factor to determine grain Zn concentrations followed by genotype and fertilizer. Depending on soil-Zn status, grain Zn concentrations could range from 8 mg kg−1 to 47 mg kg−1 in a single genotype. This strong location effect will need to be considered in estimating potential benefits of Zn biofortification. Our data furthermore showed that it was not possible to simply compensate for low soil Zn availability by fertilizer applications. In all soils fertilizer Zn was taken up as seen by a 50–200% increase in total plant Zn content. However, in more Zn deficient soils this additional Zn supply improved straw and grain yield and increased straw Zn concentrations by 43–95% but grain Zn concentrations remained largely unchanged with a maximum increase of 6%. Even in soils with high Zn status fertilizer Zn was predominantly stored in vegetative tissue. Genotypic differences in grain Zn concentrations were significant in all but the severely Zn deficient soil, with genotypic means ranging from 11 to 24 mg kg−1 in a Zn deficient soil and from 34 to 46 mg kg−1 in a high Zn upland soil. Rankings of genotypes remained largely unchanged from Zn deficient to high Zn soils, which suggests that developing high Zn cultivars through conventional breeding is feasible for a range of environments. However, it may be a challenge to develop cultivars that respond to Zn fertilizer with higher grain yield and higher grain Zn concentrations when grown in soils with low native Zn status.