R platform provides some packages that are useful to process mass spectrometry imaging (MSI) data, however, none of them provide an easy to use graphical user interface (GUI). Here, we introduce rMSI, an R package for MSI data analysis focused on providing an efficient way to manage MSI data together with a GUI integrated in R environment. MS data is loaded in rMSI custom format optimized to minimize the memory footprint yet maintaining a fast spectra access. The rMSI GUI is designed for simple and effective data exploration and visualization. Moreover, rMSI is designed to be integrated in the R environment through a library of functions that can be used to share MS data across others R packages. The release of rMSI for R environment establishes a novel and flexible platform for MSI data analysis, completely free and open-source.