Although many wireless portable devices offer more resistance to bus probing and power analysis due to their compact size, susceptibility to electromagnetic (EM) attacks must be analyzed. This paper demonstrates, for the first time, a real EM-based attack on a PDA running Rijndael and elliptic curve cryptography. A new frequency-based differential EM analysis, which computes the spectrogram, is presented. Additionally a low energy countermeasure for symmetric key cryptography is presented which avoids large overheads of table regeneration or excessive storage. Unlike previous research the new differential analysis does not require perfect alignment of EM traces, thus supporting attacks on real embedded systems. This research is important for future wireless embedded systems which will increasingly demand higher levels of security.