A novel optimisation algorithm is presented for full spectrum calibration models in near-infrared (NIR) spectroscopy. The algorithm is used to investigate the affect of removing continuous spectral regions on parameters critical to the validity of the model (e.g. explained variance, bias etc.) and ultimately identify and remove problem areas of the spectrum. As an example of its application, this paper shows how to optimise partial least squares regression (PLSR) calibration models for predicting moisture content within an intact pharmaceutical product and how problems due to changes in the nature of samples since setting up the original model may be eliminated. On application of two validated calibration models to a new set of samples unacceptable results were obtained for bias (-0.26 and -0.21% m/m moisture content) between the NIR predicted values and the true values (Karl Fischer analysis). The optimisation algorithm identified small regions of the spectrum, which if included in development of the models contributed significant bias to the final prediction. On removal of these problem regions the calibration models were found to be equally accurate and precise, but with the added advantage of robustness to a variable region of the sample spectrum (bias reduced to -0.05 and -0.09% m/m).