The traffic classification problem has recently attracted the interest of both network operators and researchers. Several machine learning (ML) methods have been proposed in the literature as a promising solution to this problem. Surprisingly, very few works have studied the traffic classification problem with Sampled NetFlow data. However, Sampled NetFlow is a widely extended monitoring solution among network operators. In this paper we aim to fulfill this gap. First, we analyze the performance of current ML methods with NetFlow by adapting a popular ML-based technique. The results show that, although the adapted method is able to obtain similar accuracy than previous packet-based methods (≈90%), its accuracy degrades drastically in the presence of sampling. In order to reduce this impact, we propose a solution to network operators that is able to operate with Sampled NetFlow data and achieve good accuracy in the presence of sampling.