We discuss the first airborne deployment and performance tests of a mid-IR difference frequency spectrometer system for highly sensitive measurements of formaldehyde. The laser system is based upon difference-frequency generation (DFG) at ~3.5 mum by mixing a DFB diode laser at 1562 nm and a distributed feedback (DFB) fiber laser at 1083 nm in a periodically poled LiNbO(3) (PPLN) crystal. Advanced LabVIEW software for lock-in, dual-beam optical noise subtraction, thermal control and active wavelength stabilization, renders a sensitivity of ~20 pptv (Absorbance ~7*10(-7)) for 30s of averaging. The instrument's performance characteristics spanning more than 300 flight hours during three consecutive airborne field missions MIRAGE, IMPEX and TexAQS operating on two airborne platforms, NCAR's C-130 and NOAA's P-3 aircraft are demonstrated.