** Sorry to resurrect an old thread, just fixed this issue and want to add it in case it helps anyone ** I built it too as I wanted the 64bit version on Fedora 22. There's a bit of an issue in the configuration, the pkg-config seems to look for libftdi.pc instead of libftdi1.pc (which is what's present on my system). I messed around a bit, one way I think to get it going is changing the "libftdi" to "libftdi1" in the configure file's following line: pkg-config --exists --print-errors "libftdi >= 0.19" that'll point pkg-config at the correct package configuration file. Another way to hack it is to make a copy of /usr/lib64/pkgconfig/libftdi1.pc called /usr/lib64/pkgconfig/libftdi.pc before running autogen.sh, configure and make. Either way I got the quick start bit file loaded then as follows (had issues with the wrapper scripts so just used the executable directly): $ sudo ./papilio-prog -v -f Quickstart-Papilio_One_250K-v1.5.bit -v Using built-in device list JTAG chainpos: 0 Device IDCODE = 0x11c1a093 Desc: XC3S250E Created from NCD file: top_avr_core_v8.ncd;UserID=0xFFFFFFFF Target device: 3s250evq100 Created: 2010/10/15 12:59:05 Bitstream length: 1353728 bits Uploading "Quickstart-Papilio_One_250K-v1.5.bit". Done. Programming time 278.1 ms USB transactions: Write 90 read 6 retries 5 A bit heavy handed I know but I don't know much about autoconf etc. and just wanted to get it building!