Aim of study: The objective was to perform an uncertainty analysis (UA) of the dynamic HORTSYST model applied to greenhouse grown hydroponic tomato crop. A frequentist method based on Monte Carlo simulation and the Generalized Likelihood Uncertainty Estimation (GLUE) procedure were used.Area of study: Two tomato cultivation experiments were carried out, during autumn-winter and spring-summer crop seasons, in a research greenhouse located at University of Chapingo, Chapingo, Mexico.Material and methods: The uncertainties of the HORTSYST model predictions PTI, LAI, DMP, ETc, Nup, Pup, Kup, Caup, and Mgup uptake, were calculated, by specifying the uncertainty of model parameters 10% and 20% around their nominal values. Uniform PDFs were specified for all model parameters and LHS sampling was applied. The Monte Carlo and the GLUE methods used 10,000 and 2,000 simulations, respectively. The frequentist method included the statistical measures: minimum, maximum, average values, CV, skewness, and kurtosis whilst GLUE used CI, RMSE, and scatter plots.Main results: As parameters were changed 10%, the CV, for all outputs, were lower than 15%. The smallest values were for LAI (10.75%) and DMP (11.14%) and the largest was for ETc (14.47%). For Caup (12.15%) and Pup (12.27%), the CV was lower than the one for Nup and Kup. Kurtosis and skewness values were close as expected for a normal distribution. According to GLUE, crop density was found to be the most relevant parameter given that it yielded the lowest RMSE value between the simulated and measured values.Research highlights: Acceptable fitting of HORTSYST was achieved since its predictions were inside 95% CI with the GLUE procedure.