City of Wisdom and Blood — Robert Merle

Montpellier in 1566 is one of the greatest seats of learning of the age, a cradle of Renaissance humanism. But even this proud city of philosophers is not safe from the menaces that endanger the peace of France--the city militia are struggling to contend with the lawlessness and religious hatred that threaten to tear the whole country in two. Only fools walk the streets at night unarmed, while a profession of faith in the wrong company can lead to a knife in the back. 
Now an adult, Pierre de Siorac must leave the family stronghold of Mespech, and travel south on dangerous roads to the great university city, accompanied by his strapping but naive brother Samson and the crafty Miroul. Well-armoured, with swords and pistols at their belts, the trio are confident of repelling any bandits who cross their path, but their new life away from the safety of their home will bring with it many other new dangers and delights.

Following on from The Brethren, City of Wisdom and Blood is the second book the sweeping saga, Fortunes of France.