A macular pigment reflectometer is handheld, light, and portable. It can be provided as a part of a self-contained system. The self-contained system includes a docking station in which the macular pigment reflectometer is placed between uses. The docking station is used to recharge the battery of the handheld macular pigment reflectometer. The docking station also has one or more types of communication ports, such as one for a wired or wireless internet connection, through which the handheld macular pigment reflectometer can communicate with a computer or an electronic medical records system. The instrument operates in a pulsed operating mode wherein relative instrument-to-eye motion is reduced and, preferably, nearly eliminated. The handheld macular pigment reflectometer contains an on-board spectrometer which is designed to capture spectra in very short intervals of time. A trigger on the instrument allows for a rapid, intuitive, and sequential alignment followed by rapid data gathering.