Aptamers are single stranded DNA or RNA ligands which can be selected for different targets starting from a huge library of molecules containing randomly created sequences. Aptamers have been selected to bind very different targets, from proteins to small organic dyes. In the last years great progress has been accomplished in the development of aptamer-based bioanalytical assays with different detection techniques. This review will describe some recent aptamer-based biosensors which have been developed for the detection of small molecules that could be interesting in the pharmaceutical field. The use of aptamers to develop assays for small molecules has not been extensively studied as for protein targets. This is mainly due to difficulties in selecting aptamers for small molecules which present fewer binding possibilities for the aptamers with respect to proteins. Despite these difficulties, a few works aiming at developing aptamer-based biosensor for small molecules have been reported which take advantage of the versatility and the flexibility of aptamers.