Where there is livestock and their food there will always be vermin, so prevention is the best form of protection. Protect yourself from disease by wearing gloves when handling dead mice and rats.
Mice: attracted by food and can get in via very small holes
Rats: attracted by food and eggs: poison or trap
Grey squirrels: attracted by food and eggs: poison or trap: worse in urban areas
Weasel or stoat: attracted by the birds: trap or prevent access
Mink: attracted by the birds: trap or prevent access
Foxes: attracted by the birds: prevent access:
Feral cats: attracted by the birds: prevent access
Magpies, crows, jackdaws and rooks: attracted by food and eggs: prevent access
Animals protected by law: owls, herons, hedgehogs.
Live catch traps are useful in case the wrong species is trapped but then there is the problem of despatching the beast. This must be done humanely and an air rifle at close range is probably the most accessible. Rat traps can also be the breakback type and must be set in a tunnel so that other species are excluded - a tunnel can be a purpose-built wooden one or a spare deep-freeze basket upended over the trap, only rats get through the bars easily. Multicatch mouse traps can be placed inside the henhouse, but remember to check and empty them, the mice tend to die overnight.
Feed and water should be inside the henhouse or a covered run. Feed should be stored in metal or plastic bins. The only open access to a hen hut during the day should be a pophole and if magpies get through this, pin vertical strips of black binbag over it - the hens will push their way in but the magpies will not like the movement of the strips. Or use a Larsen trap to catch magpies. This live-catch legal trap works by exploiting the territorial instincts of magpies. Bait it with eggs to catch the first one then put the caught bird in the decoy compartment with shelter, food and water, set the catch compartments and wait a short time to catch more magpies which can then be given to other poultry keepers to seed other Larsen traps. The best time is February to July, but can be used at other times of the year if there is a problem
Poison: keep permanent poison bait areas organized: protect from pets and children and preferably use the newer poisons which act only on rats' digestion (e.g. Eradibait), not the anticoagulants which can affect non-target species. Despite their cute antics in gardens, grey squirrels are a huge nuisance by taking food and eggs. They will eat (warfarin) poisoned maize but this must be placed in a special labelled device, again, to avoid targeting the wrong species.
Access can be prevented for foxes, cats, mink etc. by the use of fencing or covered runs. Plastic electrified netting 1.2m (4 foot) high such as Flexinet is quite useful for poultry, keeping the birds to a designated area, as long as the pulse unit is powerful. It is not 100% foox proof and can be dangerous if waterfowl get stuck in it, which they have a habit of doing.