The selection of appropriate Lexical Units (LUs) is an important issue in the development of Continuous Speech Recognition (CSR) systems. Words have been used classically as the recognition unit in most of them. However, proposals of non-word units are beginning to arise. Basque is an agglutinative language with some structure inside words, for which non-word morpheme like units could be an appropriate choice. In this work a statistical analysis of units obtained after morphological segmentation has been carried out. This analysis shows a potential gain of confusion rates in CSR systems, due to the growth of the set of acoustically similar and short morphemes. Thus, several proposals of Lexical Units are analysed to deal with the problem. Measures of Phonetic Perplexity and Speech Recognition rates have been computed using different sets of units and, based on these measures, a set of alternative non-word units have been selected.