High cost and painstaking procedures associated with fatty acid analyses of maize kernel necessitate the use of alternative methods. NIR spectroscopy offers advantages in this respect for a variety of areas such as plant breeding, food and feed industries, and biofuel production, in which different forms of maize kernel (e.g., intact kernel, flour, or oil) are used as material. We investigated the possibility of estimating maize oil quality traits by using different samples (intact kernel, flour, and oil) and conventional regression methods (multiple linear regression [MLR] and partial least squares regression [PLSR]) applied to their NIR spectra. MLR and PLSR calibration models were developed for oleic acid, linoleic acid, oleic/linoleic acid ratios, total monounsaturated fatty acid, total polyunsaturated fatty acid (PUFA), and total saturated fatty acid by analyzing 120 maize samples. Robustness in terms of prediction accuracy of the models developed here was tested with a reserved set of samples (n = 30). The results suggested that fatty acids could be possibly estimated by calibrations developed from flour and oil samples with a high degree of accuracy, whereas intact samples did not offer satisfactory results. PLSR and MLR methods gave better results in flour and oil samples, respectively. PUFA was the trait that was most successfully estimated from both flour (for the PLSR model, standard error of the estimate [SEP] of 1.78%, relative performance to deviation [RPD] of 3.09, R-2 = 0.93) and oil (for the MLR model, SEP of 0.85%, RPD of 6.52, R-2 = 0.98) samples. We concluded that sample type and chemometric method should be handled as important factors in calibration development, and the effects of these factors may vary depending on the trait being analyzed.