A growing number of long nuclear‐retained non‐coding RNAs (ncRNAs) have recently been described. However, few functions have been elucidated for these ncRNAs. Here, we have characterized the function of one such ncRNA, identified as metastasis‐associated lung adenocarcinoma transcript 1 (Malat1). Malat1 RNA is expressed in numerous tissues and is highly abundant in neurons. It is enriched in nuclear speckles only when RNA polymerase II‐dependent transcription is active. Knock‐down studies revealed that Malat1 modulates the recruitment of SR family pre‐mRNA‐splicing factors to the transcription site of a transgene array. DNA microarray analysis in Malat1‐depleted neuroblastoma cells indicates that Malat1 controls the expression of genes involved not only in nuclear processes, but also in synapse function. In cultured hippocampal neurons, knock‐down of Malat1 decreases synaptic density, whereas its over‐expression results in a cell‐autonomous increase in synaptic density. Our results suggest that Malat1 regulates synapse formation by modulating the expression of genes involved in synapse formation and/or maintenance.