With the transition to neural architectures, machine translation achieves very good quality for several resource-rich languages. However, the results are still much worse for languages with complex morphology, especially if they are low-resource languages. This paper reports the results of a systematic analysis of adding morphological information into neural machine translation system training. Translation systems presented and compared in this research exploit morphological information from corpora in different formats. Some formats join semantic and grammatical information and others separate these two types of information. Semantic information is modeled using lemmas and grammatical information using Morpho-Syntactic Description (MSD) tags. Experiments were performed on corpora of different sizes for the English–Slovene language pair. The conclusions were drawn for a domain-specific translation system and for a translation system for the general domain. With MSD tags, we improved the performance by up to 1.40 and 1.68 BLEU points in the two translation directions. We found that systems with training corpora in different formats improve the performance differently depending on the translation direction and corpora size.