Extensive guides about getting around Kyrgyzstan with car, bus, taxi, train, bicycle, and airplane have been written, see the links below. This page serves up some general recommendations.
Getting around in Kyrgyzstan
A rail connection exists between Bishkek and Moscow. Airplanes connect Osh with Bishkek. For all other places, if you do not have your own means of transport, you will be dependent on minibuses (marshrutkas) and shared taxis to take you places within Kyrgyzstan.
As soon as winter falls over Kyrgyzstan, many places hidden behind high passes become very difficult to reach over land because of snow. The passage to Osh and the Irkeshtam and Torugart passes to China can get blocked because of snow avalanches. The road to Song Kol and the Naryn-Jalalabad road are definitely closed in winter. Take possible delays into account when planning a winter trip.
Mudslides in spring are not a problem like in Tajikistan. Between May and October all parts of the country are usually easily accessible.