Tomato (Solanum lycopersicum) fruit is a model to study molecular basis of fleshy fruit development and ripening. We profiled gene expression during fruit development (immature green and mature green fruit) and ripening (breaker stage onwards) program to obtain a global perspective of genes whose expression is modulated at each stage of fruit development and ripening. A custom made cDNA macroarray containing cDNAs representing various metabolic pathways, defense, signaling, transcription, transport, cell structure and cell wall related functions was developed and used to quantify changes in the abundance of different transcripts. About 34 % of 1066 unique expressed sequence tags (ESTs) printed on the macroarray were differentially expressed during tomato fruit ripening. Out of these, 25 % genes classify under metabolism and protein biosynthesis/degradation related processes, while a significant proportion represented stress-responsive genes and about 44 % represented genes with unknown functions. RNA gel blot analysis validated changes in a few representative genes. Although the mature green fruit was found transcriptionally quiescent, the K-means cluster analysis highlighted coordinated up or down regulation of genes during progressive ripening; emphasizing that ripening is a transcriptionally active process. Many stress-related genes were found up-regulated, suggesting their role in the fruit ripening program.