Alternative splicing of pre-messenger RNAs is an important mechanism to achieve correct cellular function in higher eukaryotes. It is known that a growing number of human genetic diseases involve important splicing defects directly connected to pathologic signs. In myotonic dystrophy type 1 (DM1) it is proposed that several clinical manifestations are consequence of tissue-specific missplicing of numerous genes, triggered by a RNA gain-of-function and resultant deregulation of specific RNA-binding factors, being remarkable the nuclear sequestration of muscleblind-like family factors (MBNL1-3). Thus, identification of chemical modulators of splicing events is thought to have beneficial impacts towards the development of first valid therapy for DM1 patients. For this purpose, we generated and validated transgenic flies, which contained a luciferase reporter-based system coupled to the expression of MBNL1-reliant splicing events deregulated in DM1 patients on a relevant disease tissue (spliceosensor flies). We then developed an innovative 96-well plate screening platform to carry out in vivo high throughput pharmacological screening (HTS) with the spliceosensor model. After a large-scale evaluation (>16,000 chemical entities) several reliable splicing modulators (hits) were identified. Hit validation steps recognized separate DM1-linked therapeutic traits for some of them, which corroborated the feasibility of the approach described herein for revealing promising drug candidates by indirect improving of DM1 missplicing. The powerful Drosophila-based tool for innovative chemical screening is suitable for its use with other disease models displaying abnormal alternative splicing coupled to a luminescent reporter-based system as final read-out, thus offering widespread uses in drug discovery.