Polyphosphoinositides (PIP) and (PIP2) show prominent negative singly and doubly charged deprotonated molecules in electrospray mass spectrometry. These ions can be used for quantification of PIP and PIP2 in the low picomole range, without prior chromatographic separation, using selected ion monitoring and consecutive measurements of the signals from the deprotonated singly charged molecules. The dose response curves for both compounds are linear. In a complex matrix consisting of polar lipids (Folch extract) PIP and PIP2 monitored at m/z 965.4 and 1045.5 (stearoyl and arachidonoyl) were determined in the low picomole range, at a flow rate of 100 μL/min. Collision-induced decomposition of PIP and PIP2 using a mixture of xenon and argon at 25 eV afforded identical high mass ions formed by loss of a molecule of water from PIP and a phosphate group and a molecule of water from PIP2. The results indicate that polyphosphoinositides, and biologically relevant changes in their concentrations, can be quantified directly in cells and cellular membranes by selected-ion monitoring with electrospray mass spectrometry.